Genetic Variation In Natural Populations Research Articles

Towards the understanding of genetic and morphological variations of a highly abundant seaweed-associated marine invertebrate

Unraveling the patterns of genetic structure and demographic history of marine species, as well as the factors that shape their genetic variations, is fundamental for informing conservation strategies for species and their environments. In this work, we investigate the current population structure and historical demographic patterns of the conspicuous seaweed-associated amphipod Hyale niger at a fine spatial scale in the subtropical SW Atlantic coast, in Brazil, by using both genome-wide and mitochondrial DNA markers. We also investigate how geographic distance, current oceanographic conditions, and variations in a key morphological trait contribute to the genetic variability of the amphipod. We observed an evident population genetic structure, even at a fine spatial scale, although genetic differentiation was lower than our expectations for a benthic direct brooder. Demographic history inferences were consistent across populations and showed two major demographic expansions on interglacial periods during the late Pleiostocene, before and after the last glacial maximum. We also demonstrated that isolation-by-environment (IBE) was the main driver of genetic differentiation, although we could not separate it from the effects of isolation-by-distance (IBD). Among environmental factors, nutrient concentrations in seawater were most relevant for explaining genetic structure. In addition, our data suggest that morphological variation in gnathopod 2 structure of males were not genetic-related and were probably plastic as a response to variations in macroalgae frond size. Our study reinforces the importance of using multiple molecular markers and analytical approaches to unveil patterns and processes generating genetic variation in natural populations.

New Chloroplast Microsatellites in Helichrysum italicum (Roth) G. Don: Their Characterization and Application for the Evaluation of Genetic Resources

Helichrysum italicum (Roth) G. Don is a Mediterranean medicinal plant with great potential in the cosmetics, culinary and pharmaceutical fields due to its unique bioactive compounds. Its recent introduction into agroecosystems has enhanced the exploitation of genetic diversity in natural populations, although limited molecular markers have made this challenging. In the present study, primers were designed for all 43 SSRs (72.1% mononucleotide, 21% dinucleotide and 6.9% trinucleotide repeats) identified in the chloroplast genome. Populations from Cape Kamenjak (Croatia) and Corsica (France) were analyzed with ten carefully selected cpSSR markers. From the initial set of 16 cpSSRs amplified in all samples, 6 cpSSR markers were removed due to low-length polymorphisms, size homoplasy and nucleotide polymorphisms that could not be detected with allele length. Of the 38 haplotypes detected, 32 were unique to their geographic origin. The highest number of private haplotypes was observed in the Cape Kamenjak population (seven out of nine detected). Based on clustering analyses, the Kamenjak population was the most similar to the Capo Pertusato (south Corsica) population, although only one sub-haplotype was shared. Other Corsican populations were more similar to each other. A cross-species transferability test with Helichrysum litoreum Guss. and Helichrysum arenarium (L.) Moench was successfully conducted and private alleles were identified.

Constraining models of dominance for nonsynonymous mutations in the human genome.

Dominance is a fundamental parameter in genetics, determining the dynamics of natural selection on deleterious and beneficial mutations, the patterns of genetic variation in natural populations, and the severity of inbreeding depression in a population. Despite this importance, dominance parameters remain poorly known, particularly in humans or other non-model organisms. A key reason for this lack of information about dominance is that it is extremely challenging to disentangle the selection coefficient (s) of a mutation from its dominance coefficient (h). Here, we explore dominance and selection parameters in humans by fitting models to the site frequency spectrum (SFS) for nonsynonymous mutations. When assuming a single dominance coefficient for all nonsynonymous mutations, we find that numerous h values can fit the data, so long as h is greater than ~0.15. Moreover, we also observe that theoretically-predicted models with a negative relationship between h and s can also fit the data well, including models with h = 0.05 for strongly deleterious mutations. Finally, we use our estimated dominance and selection parameters to inform simulations revisiting the question of whether the out-of-Africa bottleneck has led to differences in genetic load between African and non-African human populations. These simulations suggest that the relative burden of genetic load in non-African populations depends on the dominance model assumed, with slight increases for more weakly recessive models and slight decreases shown for more strongly recessive models. Moreover, these results also demonstrate that models of partially recessive nonsynonymous mutations can explain the observed severity of inbreeding depression in humans, bridging the gap between molecular population genetics and direct measures of fitness in humans. Our work represents a comprehensive assessment of dominance and deleterious variation in humans, with implications for parameterizing models of deleterious variation in humans and other mammalian species.

Continuously fluctuating selection reveals fine granularity of adaptation.

Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown1,2. Here we generated genome-wide allele frequency data every 1-2 generations from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December (a period of approximately 12 total generations). Adaptation throughout the fundamental ecological phases of population expansion, peak density and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of change in allele frequency to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveala fitness relevance of standing variation that is likely to be masked by inference approaches based on static population sampling or insufficiently resolved time-series data. We propose that such fine-scaled, temporally fluctuating selection may be an important force contributing to the maintenance of functional genetic variation in natural populations and an important stochastic force impacting genome-wide patterns of diversity at linked neutral sites, akin to genetic draft.

Evaluation of industrial and consumer 3-D resin printer fabrication of microdevices for quality management of genetic resources in aquatic species

Aquatic germplasm repositories can play a pivotal role in securing the genetic diversity of natural populations and agriculturally important aquatic species. However, existing technologies for repository development and operation face challenges in terms of accuracy, precision, efficiency, and cost-effectiveness, especially for microdevices used in gamete quality evaluation. Quality management is critical throughout genetic resource protection processes from sample collection to final usage. In this study, we examined the potential of using three-dimensional (3-D) stereolithography resin printing to address these challenges and evaluated the overall capabilities and limitations of a representative industrial 3-D resin printer with a price of US$18,000, a consumer-level printer with a price <US$700, and soft lithography, a conventional microfabrication method. A standardized test object, the Integrated Geometry Sampler (IGS), and a device with application in repository quality management, the Single-piece Sperm Counting Chamber (SSCC), were printed to determine capabilities and evaluate differences in targeted versus printed depths and heights. The IGS design had an array of negative and positive features with dimensions ranging from 1 mm to 0.02 mm in width and depth. The SSCC consisted of grid and wall features to facilitate cell counting. The SSCC was evaluated with polydimethylsiloxane (PDMS) devices cast from a typical photoresist and silicon mold. Fabrication quality was evaluated by optical profilometry for parameters such as dimensional accuracy, precision, and visual morphology. Fabrication time and cost were also evaluated. The precision, reliability, and surface quality of industrial-grade 3-D resin printing were satisfactory for operations requiring depths or heights larger than 0.1 mm due to a low discrepancy between targeted and measured dimensions across a range of 1 mm to 0.1 mm. Meanwhile, consumer-grade printers were suitable for microdevices with depths or heights larger than 0.2 mm. While the performance of either of these printers could be further optimized, their current capabilities, broad availability, low cost of operation, high throughput, and simplicity offer great promise for rapid development and widespread use of standardized microdevices for numerous applications, including gamete quality evaluation and “laboratory-on-a-chip” applications in support of aquatic germplasm repositories.

Molecular evidence for a new endemic species of Acartia (Copepoda, Calanoida) from the Southeast Pacific coast

The loss of biodiversity in marine populations is one of the consequences of the increased events of extreme environmental conditions in the oceans, which can condition the persistence of populations to future scenarios of climate change. Therefore, it is extremely necessary to explore and monitor the genetic diversity of natural populations. In the Southeast Pacific Ocean (SEPO), specifically on the coast of Chile, the presence of the copepod Acartia tonsa has been indicated solely using morphological evidence, due to the absence of genetic information. In the present work, the genetic diversity, population structure and phylogenetic position within the genus Acartia, of populations identified morphologically as A. tonsa, was evaluated by amplification of the mitochondrial cytochrome c oxidase subunit I and nuclear marker 18 s. Our results showed that the populations identified as A. tonsa correspond to a new monophyletic group endemic to SEPO (GMYC = 1.00; PTP = 0.95). The populations showed moderate to high genetic diversity with an incipient structuring between populations and biogeographic zones. Our results suggest that despite the homogenizing effect of the Humboldt Current, isolation by distance and contrasting environmental conditions at different geographic scales have an important influence on the genetic diversity of zooplankton in the SEPO region.

Polymorphism and the Red Queen: the selective maintenance of allelic variation in a deteriorating environment.

Although allelic variation is ubiquitous in natural populations, our theoretical models are poor at predicting the existence and properties of these observed polymorphisms. In this study, inspired by Van Valen's Red Queen hypothesis, we modeled the effect of viability selection in a deteriorating environment on the properties of allelic variation in populations subject to recurrent mutation. In Monte Carlo simulations, we found that levels of polymorphism consistently built up over time. We censused the simulated populations after 10,000 generations of mutation and selection, revealing that, compared with models assuming a constant environment, the mean number of alleles was greater, as was the range of allele numbers. These results were qualitatively robust to the addition of genetic drift and to the relaxation of the assumption that the viabilities of phenogenotypes containing a new mutation are independent of each other (i.e. incorporating a model of generalized dominance). The broad range of allele numbers realized in the simulated populations-from monomorphisms to highly polymorphic populations-more closely corresponds to the observed range from numerous surveys of natural populations than previously found in theoretical studies. This match suggests that, contrary to the views of some writers, selection may actively maintain genetic variation in natural populations, particularly if the selective environment is gradually becoming harsher. Our simulations also generated many populations with heterozygote advantage, a mismatch with real data that implies that this selective property must arise extremely rarely in natural populations.

Spatial Pattern of Genetic Diversity and Demographic History Revealed by Population Genomic Analysis: Resilience to Climate Fluctuations of Acer truncatum Bunge

Whole genome sequencing techniques are capable of providing insights into plant genetic adaptation to climate oscillations. Acer truncatum Bunge is a new resource tree for food with ornamental, timber and medicinal value. However, it has been listed as a near-threatened species because of the decreasing number of natural populations. In order to develop conservation strategies and sustainable innovative utilization for genetic resources, spatial pattern of genetic diversity and demographic history of A. truncatum from 13 natural populations, which cover the entire range, were analyzed by 9,086,353 single nucleotide polymorphisms (SNPs) through whole genome resequencing. The genetic diversity of natural populations was high (He = 0.289, I = 0.449), and genetic variations mainly resided within populations (82.47%) by AMOVA analysis. Cluster analysis showed that 13 natural populations mainly originated from three common gene pools. Therefore, it is recommended that the natural populations (LBGM, BTM, WLS and DQT) with high genetic diversity in different groups were given priority for in situ conservation and the genetic resources from these populations were collected for ex situ conservation. The effective population size of A. truncatum experienced two large-scale sharp contractions and currently decreased to its bottom in history. Nonetheless, A. truncatum could have expanded its effective population size to its historical peak after the last glacial period, indicating that it is highly resilient to fluctuations of temperature and humidity.

Local scale extreme low pH conditions and genetic differences shape phenotypic variation in a broad dispersal copepod species

Extreme low pH events in estuaries and upwelling areas can modulate the phenotypic and genetic diversity of natural populations. To test this hypothesis, we explored the linkage between local scale extreme low pH events, genetic diversity, and variation in fecundity-related traits (body size, egg size, and egg production rate) in the broad-dispersal copepod Acartia tonsa. We assessed genetic and phenotypic characteristics of populations by contrasting extreme low pH environments (upwelling and temperate estuary) in the coastal Southeast Pacific, under natural and experimental conditions. These populations showed significant genetic differentiation with higher diversity in mitochondrial and nuclear loci (encoding mtCOI and 18S rRNA) in the estuarine population. Copepods from this population are exposed to more frequent extreme low pH events (&amp;lt; 7.7), and the adult females exhibit consistent phenotypic variation in body size, egg size, and egg production rate across different cohorts. Experimental acclimation to extreme low pH conditions revealed no significant differences in fecundity-related traits between A. tonsa populations. Although these results partially support our hypothesis, the experimental findings suggest other drivers might also influence phenotypic differences in the local environments.

Genetic Diversity in Natural Populations of the Near-Threatened Species Lignobrycon myersi (Characiformes, Triportheidae): Implications for Species Conservation.

The river basins of Brazil contain a highly diverse ichthyofauna of remarkable endemism, including several threatened species. Accordingly, Lignobrycon myersi is a fish species distributed only in a few rivers from the state of Bahia, northeastern Brazil. Since this species is classified as Near Threatened and is poorly studied, efforts to understand the genetic structure of populations and putative cryptic forms should help define efficient strategies of management and conservation. Herein, the molecular identification and the population genetic diversity of specimens of L. myersi across their range (Almada, Contas, and Cachoeira river basins) were assessed using mitochondrial markers (16S rDNA and D-Loop, respectively). The inferences based on phylogenetics, genetic distance, and species delimitation methods invariably identified all samples as L. myersi. In addition, sequencing of D-loop fragments revealed significant haplotype diversity and a considerable level of population genetic structure. Despite their geographic isolation, these data suggested that populations from Almada and Contas rivers represent a single evolutionary lineage that could be managed as a whole. In contrast, the population from Cachoeira River was highly differentiated from the others and should be managed separately as a unique and endemic unit, particularly focused on the conservation of native habitats.

Chemical and genetic diversity of Baccharis dracunculifolia DC. (Asteraceae) from the Cerrado biome

The essential oil of four populations of Baccharis dracunculifolia was analyzed for their chemical composition by CG/MS and the study of genetic diversity was conducted by analyzing the DNA polymorphism using microsatellite markers. The predominant compounds were E-nerolidol, cis-β-guaiene, germacrene D, E-caryophyllene, limonene, α-pinene, β-myrcene, δ-cadinene, β-pinene and spathulenol. The E-nerolidol substance was the most abundant among the compounds present in the essential oil in all populations. Genetic analysis showed that most of the diversity of B. dracunculifolia was within populations, and the diversity among populations is not expressive. All the populations evaluated in this study were in a process of extensive fragmentation, this might be the main cause of reduced genetic diversity of this specie in Cerrado biome. The comparison between PCA of genotypes and chemodiversity reinforces the unique profile for each population despite the environmental similarity observed and genetic analysis. The results obtained in this work, using microsatellite markers, made it possible to assess the genetic variability in natural populations of B. dracunculifolia.

DIVERSIDAD DEL MAÍZ EN TRES ZONAS GEOMORFOLÓGICAS DE YUCATÁN, MÉXICO

&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Maize (&lt;em&gt;Zea mays&lt;/em&gt; L.) is the main sustenance in the daily diet of Mexican families. As a crop, it is one of the most important in the country of Mexico, and in Yucatan state, it is grown under rainfed conditions in milpas with no mechanizable lands. In this study, an analysis of the phenotypic variability from cob collects of native maize from Yucatan state was carried out, with ethnobotanical information collected within passport data. &lt;strong&gt;Objectives:&lt;/strong&gt; To introduce the genetic diversity of maize into a germplasm bank, to know the genetic diversity of native populations based on the characteristics of cob, to know its distribution, to find the potential populations in each collection area for its use in genetic improvement programs. &lt;strong&gt;Methodology: &lt;/strong&gt;66 Tuxpeños, 13 Dzit bacal, 6 Nal tel, 13 Xmejen nal, and 2 Nal xoy were collected in the southern, central, and eastern regions of the state, from January to March 2020, by sampling the four cardinal points in each community visited. A vector map of collections in Yucatan was developed and quantitative data of 13 biometric cob variables were recorded in 100 populations (crop cycles: late n=68; intermediate n=26; early n=6), a general data analysis of variance (ANOVA) and by crop cycles were made, principal component analysis (PCA), hierarchically clustered with the average linkage method and discriminant analysis were made. Qualitative data from ethnobotanical surveys with mixed questions applied to milperos at the time of collection are presented. &lt;strong&gt;Results: &lt;/strong&gt;The diversity of native maize in Yucatan is made up of three main groups based on the crop cycle: late, intermediate, and early. The southern and eastern regions of Yucatan preserve greater diversity, representing 44 and 40% of the total collections, respectively. There were significant differences in all ear variables; in a late growth cycle, only the grain thickness did not show differences between populations, and in the early growth cycle the grain thickness, width, and length variables were not significant. The PCA explained 80% of the total variation, seven different groups were formed, with greater differentiation in early maize Nal tel, intermediate Xmejen nal and Dzit bacal, contrary to the Tuxpeños late maize. Ten promising populations were identified for selection in each geomorphological region: eight correspond to the southern, two to the eastern, and one to the center of Yucatan state. The main factors to select for sowing corn in the region are: white and yellow maize for yield, the resistance to weevil attack for red maize, and the perception of color and palatability in purple maize. &lt;strong&gt;Implications: &lt;/strong&gt;A complete phenotypic characterization in the field is required with a special interest in red-pigmented maize.&lt;strong&gt; Conclusions: &lt;/strong&gt;The interest of the milperos in conserving and sowing the different native maize are based on the color of the grain, the benefits and uses that they can obtain from them, which determine the planting area in the milpas of the different races/varieties of maize. Red grain maize is being planted in a lower area in relation to other colors. The southern and eastern geomorphological regions showed a genetic flow between them.&lt;/p&gt;

Differentiation and decreased genetic diversity in field contaminated oysters Crassostrea hongkongensis: Identification of selection signatures

The extent to which chemical contamination affects the population structure and genetic diversity of natural populations remains elusive. Here, we used the whole-genome resequencing and transcriptome to diagnose the effects of long-term exposure to multiple elevated chemical pollutants on the population differentiation and genetic diversity in oysters Crassostrea hongkongensis in a typically polluted Pearl River Estuary (PRE) of Southern China. Population structure revealed an obvious differentiation between the PRE oysters and those collected from a nearby clean Beihai (BH) individuals, while no significant differentiation was observed among individuals collected from the three pollution sites within PRE due to the high gene flow. The decreased genetic diversity in the PRE oysters reflected the long-term effects of chemical pollutants. Selective sweeps between BH and PRE oysters revealed that chemical defensome genes, including glutathione S-transferase, zinc transporter, were responsible for their differentiation, sharing common metabolic process of other pollutants. Combined with the genome-wide association analysis, 25 regions containing 77 genes were identified to be responsible for the direct selection regions of metals. Linkage disequilibrium blocks and haplotypes within these regions provided the biomarkers of permanent effects. Our results provide important insights to the genetic mechanisms underlying the rapid evolution under chemical contamination in marine bivalves.

Tropical forest loss and geographic location drive the functional genomic diversity of an endangered palm tree.

Human activity has diminished forests in different terrestrial ecosystems. This is well illustrated in the Brazilian Atlantic Forest, which still hosts high levels of species richness and endemism, even with only 28% of its original extent remaining. The consequences of such forest loss in remaining populations can be investigated with several approaches, including the genomic perspective, which allows a broader understanding of how human disturbance influences the genetic variability in natural populations. In this context, our study investigated the genomic responses of Euterpe edulis Martius, an endangered palm tree, in forest remnants located in landscapes presenting different forest cover amount and composed by distinct bird assemblage that disperse its seeds. We sampled 22 areas of the Brazilian Atlantic Forest in four regions using SNP markers inserted into transcribed regions of the genome of E.edulis, distinguishing neutral loci from those putatively under natural selection (outlier). We demonstrate that populations show patterns of structure and genetic variability that differ between regions, as a possible reflection of deforestation and biogeographic histories. Deforested landscapes still maintain high neutral genetic diversity due to gene flow over short distances. Overall, we not only support previous evidence with microsatellite markers, but also show that deforestation can influence the genetic variability outlier, in the scenario of selective pressures imposed by these stressful environments. Based on our findings, we suggest that, to protect genetic diversity in the long term, it is necessary to reforest and enrich deforested areas, using seeds from populations in the same management target region.

Genomics reveal the origins and current structure of a genetically depauperate freshwater species in its introduced Alaskan range.

Invasive species are a major threat to global biodiversity, yet also represent large-scale unplanned ecological and evolutionary experiments to address fundamental questions in nature. Here we analyzed both native and invasive populations of predatory northern pike (Esox lucius) to characterize landscape genetic variation, determine the most likely origins of introduced populations, and investigate a presumably postglacial population from Southeast Alaska of unclear provenance. Using a set of 4329 SNPs from 351 individual Alaskan northern pike representing the most widespread geographic sampling to date, our results confirm low levels of genetic diversity in native populations (average 𝝅 of 3.18 × 10-4) and even less in invasive populations (average 𝝅 of 2.68 × 10-4) consistent with bottleneck effects. Our analyses indicate that invasive northern pike likely came from multiple introductions from different native Alaskan populations and subsequently dispersed from original introduction sites. At the broadest scale, invasive populations appear to have been founded from two distinct regions of Alaska, indicative of two independent introduction events. Genetic admixture resulting from introductions from multiple source populations may have mitigated the negative effects associated with genetic bottlenecks in this species with naturally low levels of genetic diversity. Genomic signatures strongly suggest an excess of rare, population-specific alleles, pointing to a small number of founding individuals in both native and introduced populations consistent with a species' life history of limited dispersal and gene flow. Lastly, the results strongly suggest that a small isolated population of pike, located in Southeast Alaska, is native in origin rather than stemming from a contemporary introduction event. Although theory predicts that lack of genetic variation may limit colonization success of novel environments, we detected no evidence that a lack of standing variation limited the success of this genetically depauperate apex predator.

Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value.

Spatial patterns of genetic variation compared across species provide information about the predictability of genetic diversity in natural populations, and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni- a major river system from the Guiana Shield -, to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, the mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as gold mining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow, and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.

Genetic Diversity in Natural Populations of Rhodiola Species of Different Adaptation Strategies.

Representatives of the Crassulaceae family's genus Rhodiola are succulents, making them distinctive in a changing environment. One of the most significant tools for analyzing plant resources, including numerous genetic processes in wild populations, is the analysis of molecular genetic polymorphism. This work aimed to look at the polymorphisms of allelic variations of the superoxide dismutase (SOD) and auxin response factor (ARF) gene families, as well as the genetic diversity of five Rhodiola species, using the retrotransposons-based fingerprinting approach. The multi-locus exon-primed intron-crossing (EPIC-PCR) profiling approach was used to examine allelic variations in the SOD and ARF gene families. We implemented the inter-primer binding site (iPBS) PCR amplification technique for genome profiling, which demonstrated a significant level of polymorphism in the Rhodiola samples studied. Natural populations of Rhodiola species have a great capacity for adaptation to unfavorable environmental influences. The genetic variety of wild populations of Rhodiola species leads to their improved tolerance of opposing environmental circumstances and species evolutionary divergence based on the diversity of reproductive systems.

Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster.

Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to sampling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a genome-wide association studies in three genes: dachsous, extra-macrochaete, and neuralized, using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the dachsous shape change vector, we observe genetic differentiation of variants in dachsous and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the extra-macrochaete shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of dachsous, suggesting that the available genetic diversity of a population, summarized by the genetic (co)variance matrix (G), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.

Chloroplast genomic characterization and phylogenetic analysis of Castanopsis hystrix

The structure and size of the chloroplast genome of Castanopsis hystrix was determined by Illumina HiSeq 2500 sequencing platform to understand the difference between C. hystrix and the chloroplast genome of the same genus, and the evolutionary position of C. hystrix in the genus, so as to facilitate species identification, genetic diversity analysis and resource conservation of the genus. Bioinformatics analysis was used to perform sequence assembly, annotation and characteristic analysis. R, Python, MISA, CodonW and MEGA 6 bioinformatics software were used to analyze the genome structure and number, codon bias, sequence repeats, simple sequence repeat (SSR) loci and phylogeny. The genome size of C. hystrix chloroplast was 153 754 bp, showing tetrad structure. A total of 130 genes were identified, including 85 coding genes, 37 tRNA genes and 8 rRNA genes. According to codon bias analysis, the average number of effective codons was 55.5, indicating that the codons were highly random and low in bias. Forty-five repeats and 111 SSR loci were detected by SSR and long repeat fragment analysis. Compared with the related species, chloroplast genome sequences were highly conserved, especially the protein coding sequences. Phylogenetic analysis showed that C. hystrix is closely related to the Hainanese cone. In summary, we obtained the basic information and phylogenetic position of the chloroplast genome of red cone, which will provide a preliminary basis for species identification, genetic diversity of natural populations and functional genomics research of C. hystrix.

Modeling the genetic footprint of fluctuating balancing selection: from the local to the genomic scale.

Natural selection not only affects the actual loci under selection but also leaves "footprints" in patterns of genetic variation in linked genetic regions. This offers exciting opportunities for inferring selection and for understanding the processes shaping levels of genetic variation in natural populations. Here, we develop analytical approximations based on coalescent theory to characterize the genetic footprint of a complex, but potentially common type of natural selection: balancing selection with seasonally fluctuating allele frequencies. As we show analytically and confirm with stochastic simulations, seasonal allele frequency fluctuations can have important (and partly unexpected) consequences for the genetic footprint of balancing selection. Fluctuating balancing selection generally leads to an increase in genetic diversity close to the selected site, the effect of balancing selection, but reduces diversity further away from the selected site, which is a consequence of the allele-frequency fluctuations effectively producing recurrent bottlenecks of allelic backgrounds. This medium- and long-range reduction usually outweighs the short-range increase when averaging diversity levels across the entire chromosome. Strong fluctuating balancing selection even induces a loss of genetic variation in unlinked regions, e.g. on different chromosomes. If many loci in the genome are simultaneously under fluctuating balancing selection this can lead to substantial genome-wide reductions in genetic diversity, even when allele-frequency fluctuations are small and local footprints are difficult to detect. Thus, together with genetic drift, selective sweeps and background selection, fluctuating selection could be a major force shaping levels of genetic diversity in natural populations.